rs2965261

Variant names:

• chr19-53272433-G-A
• rs2965261

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.243 in 151,948 control chromosomes in the GnomAD database, including 4,722 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.24 (4722 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.17
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36935 AN: 151830 Hom.: 4721 Cov.: 31

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.258

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.243 AC: 36951 AN: 151948 Hom.: 4722 Cov.: 31 AF XY: 0.245 AC XY: 18180 AN XY: 74246

African (AFR) AF: 0.156 AC: 6456 AN: 41478

American (AMR) AF: 0.247 AC: 3770 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1168 AN: 3466

East Asian (EAS) AF: 0.347 AC: 1789 AN: 5154

South Asian (SAS) AF: 0.214 AC: 1029 AN: 4808

European-Finnish (FIN) AF: 0.292 AC: 3074 AN: 10526

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.278 AC: 18857 AN: 67938

Other (OTH) AF: 0.256 AC: 540 AN: 2106

Alfa AF: 0.270 Hom.: 10262

Bravo AF: 0.240

Asia WGS AF: 0.266 AC: 924 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.64
DANN	Benign	0.35
PhyloP100		-4.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2965261; hg19: chr19-53775686;